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Full NGIS release notes can be found here.

What's New in the CIP-API?

Nembus Increment - December 2024
  • A new column has been added to daily email notifications to indicate if a case was previously archived (CIPAPI-2396).
  • The "Cancer bridge DSS" button has been renamed to "Cancer DSS" for clarity (INTPORTAL-1908).
  • A tag will now be generated when a tiered variant is missing in Congenica due to an Ensembl discrepancy. For more information, see here (CIPAPI-2416).
  • The Portal now supports the most recent gene panel updates for Autumn 2024 release (IP-5524)
Nembus - October 2024
  • The Portal has been upgraded to use Cellbase version 5 for all annotation datasets. This update enhances several features, including Show Variant Details, ClinVar Classifications, Add Variants from VCF, Max Allele Frequencies, and Summary of Findings. For more information, see here.
Warning

During our integration testing with Congenica we identified a scenario where cases may fail to process in Congenica due to Ensembl versions no longer aligning between GeL and Congenica after the CellBase upgrade.

Immediately post Nembus release it has been agreed with NHSE that any impacted referrals will be dealt with manually, then as part of the Nembus Increment release, Congenica will add functionality to "tag" details of tiered variants that fail to load in their application.

Tag information, if required, will then be made available to TPIs from the exisiting "tags" field in interpretation request endpoint.

Further information will be provided when Nembus Increment is released on how users can understand the tags.

  • Unified tiering for CNVs, STRs, and small variants is now available in the Interpretation Portal, improving the display of compound heterozygotes. For more details, see here.
  • The Portal now supports the latest gene panel updates for Test Directory v7 (IP-5482).
  • A fix has been implemented to ensure that cases are flagged correctly in the Daily Summary Emails (IP-5230).
Mira - April 2024

Please be advised that after deployment, a final hard refresh is required to clear your browser cache. Subsequent deploys will not need this action.

  • Cancer sample and variant information is no longer shown in the Interpretation Portal to prevent redundancy with the Cancer DSS (INTPORTAL-1776, INTPORTAL-1775).
  • Prospective referrals, processed in the RD pipeline with Dragen v4, can now displayed in the Interpretation Portal (INTPORTAL-1744, CIPAPI-2145).
  • Users can now download STR plots from the Portal in SVG format instead of PNG (INTPORTAL-1744).
  • The Portal now supports the most recent gene panel updates for Test Directory v6 (IP-5377).
  • The HGVS field in the Summary of Findings HTML is now sourced from Cellbase (CIPAPI-941).
  • Editing the RoQ will no longer cause a referral to be moved to the "Reported Cases" tab if there's a newer RoQ in draft state (CIPAPI-1225).
  • The Portal has been upgraded to incorporate version 8.5.0 of GRM for GMS RD and 8.6.0 for Cancer referrals (IP-5416), this means that the Portal will support features of Tumour Only referrals (CIPAPI-2011) when these arrive.
  • BSVI has been decommissioned, as a result, users will no longer be able to access it.
Lyra Hotfix - February 2024
  • Resolves a bug related to the submission of Reporting Outcomes Questionnaires that were auto-populated for VUS variants (INTPORTAL-1805)
Lyra - December 2023
  • The first stage of the Reporting Outcommes Questionnaires (ROQs) improvements has been completed. The Portal now ofers a new feature to auto-populate certain questions from the ROQ with the information previously entered during decision-making in Congenica. Learn more here (INTPORTAL-1645).
  • The gnomAD link from the Interpretation Browser now navigates to v4.0.0 (INTPORTAL-1788).
  • The SNP check has been removed from the Case Dispatch Workflow. Refer to the SMS Help Page for more information.
Kraz - November 2023
  • The Portal now offers the ability to interpret cases using the Cancer DSS. For more details on the impact on the Portal, please refer to the Cancer DSS Quickstart Guide.
  • We have updated the PanelApp URLs. All links from the Portal will now redirect to https://panelapp.genomicsengland.co.uk/.
  • The Genomics England address displayed in the Portal has been updated to reflect the current information.
Jabbah - September 2023
  • The default score for the Exomiser filter has been changed to =>0.75 from >0.75 (INTPORTAL-1690).
  • The Download TSV file button for the SNV table now displays the list of variants (INTPORTAL-1716).
  • The sort order for CVA Classifications is now working as expected; Pathogenic > Likely Pathogenic > Conflicting Classifications > VUS > Likely Benign > Benign > Unclassified (INTPORTAL-1707).
  • The CVA links to variants and ClinVar annotations are now loaded to variants when using the Add variants from VCF feature (IP-5207).
  • Now, after using the Add variants from VCF feature, the user sees the Filter Tiered Variants filter engaging with the selected gene and only the variants for this selected gene are visible in the SNV variant table (INTPORTAL-1704).
Izar Increments - May 2023 and July 2023

May 2023:

  • Enables link out to Cancer Bridge DSS along side link to BSVI
  • Fixes Exomiser variant soring bug in the Interpretation Browser
  • Security vulnerability and cellbase client updates in the backend (SMS and CIP-API)
  • Updated link out:
    • Improved DECIPHER links for CNVs on the CNV call level table. Now there is one for the phenotype and one for the genome browser
    • Added links to Splice AI, OMIM and VarSome from variants on the SNV table
  • Fixed Test Tumour Diagnosis Date displaying incorrectly
  • Added a visual aid to quickly discriminate between rare and more common CNVs (gains and losses) based on population frequency
    • Loss columns: CNVs with a LOSS frequency % less than 0.5% are shaded in red. CNVs with a LOSS frequency % greater than or equal to 0.5% are not shaded red
    • Gain columns: CNVs with a GAIN frequency % less than 1% are shaded in red. CNVs with a GAIN frequency % greater than or equal to 1% are not shaded red

July 2023:

  • Session Management - Learn more about the changes here
Izar - March 2023
  • Performance improvements returning CVA annotations to the Interpretation Browser (INTPORTAL-1460)
  • Known Pathogenic Variant Prioritisation (KPVP) updates to the Interpretation Browser (IP-4603)

Bioinformatics Pipeline updates will mean known pathogenic variants from ClinVar, that previously may have been filtered out, will now be prioritised by Genomics England Tiering.

To support interpretation of KPVP results, the Interpretation Browser has added a new "ClinVar Classifications" column that allows users to more easily review and access ClinVar annotations.

For further information on KPVP please see here.

And for a full demo of Izar release see the recording here

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Hercules Increment - January 2023
  • The Interpretation Browser now contains links to DECIPHER, gnomAD and UCSC
  • Variant read depth is displayed in the Interpretation Browser
  • There's a new variant copy button that copies variant details into Alamut format for easier pasting
  • The STR sorting has been improved and there is a new STR filter
  • When users filter variants based on Exomiser score the default filter value has changed to 0.75
  • See here for more info on these changes
Grace - November 2022
  • The Interpretation Portal is now displaying Tier Null STRs. More information here, including a demo video.
  • The warning that FMR1 variants are not reported in STR report events has been updated to only be shown if FMR1 variants are indeed not reported, so that users don't incorrectly assume FMR1 STRs are not reported. More information here.
  • A new scenario has been included in The Diagnostic Discovery video to help users navigate through cases with non-PASS variants. Watch it here.
  • The landing page of the Portal Help Page now displays an introductory video to the Interpretation Portal's role in the GMS. Watch it here.
  • New files associated with cancer referrals available for download. Including, annotated VCF for small variants, germline CNV/SV VCF, somatic CNV/SV CSV, BAF for tumour samples. Please refer to the Cancer Genome Analysis Guide for further information

Coming up next

Upcoming Features and Enhancements

  • Editable Exit Questionnaires will soon be available directly from the Cancer DSS. More details on how this will impact case closures will be shared shortly.

  • We are introducing b-allele frequency plots for CNV mosaic detection, aligned with updates from the Rare Disease pipelines.

  • The processing of Exomiser will be transitioned to the Rare Disease pipelines. Further information on how this will affect case workflows will be provided soon.

  • We are moving to a numeric tiering system for CNVs to enhance classification and reporting consistency.

  • The Portal's authentication will be streamlined to align with other GEL applications, so users no longer need to manually enter their passwords or emails.

Warning
  • If a user has multiple accounts open, the system will ask you to choose between one of them on refresh.
  • CVA still requires users to manually enter their username and password.

For more information on providing feedback, click here.

Last update: 2024-12-02